How do I identify motifs in a protein sequence

InterProscan performs a functional analysis of a protein sequence by searching it against the InterPro database. This is a collection of protein domain and family models, called signatures, that try to predict the function of your protein by classifying it into a particular protein family and identify particular domains and other interesting sites in the sequence. InterPro signatures comprise profiles/motifs from many different protein domain/family databases.

To search a protein sequence against InterProScan.

• Choose DATABASE | INTERNET INTERPROSCAN SEARCH menu item.
• Wait until the job has finished, or hit CLOSE to let the job run in the background with the Job Manager.
• The results will appear in the Results Window or should be double clicked in the Job Manager to view them.
• In the Results tab any clickable link will appear in an external browser (e.g. Safari). If you click the Green Cross the domain will be annotated to your sequence.

All InterProScan results that are annotated to a protein sequence will have the Feature Type of "PROTEIN MATCH". This is NOT a valid GenPept keyword. You will need to manually curate any added annotation to choose the appropriate GenPept KeyWord.

See How do I Align Sequences help topic for an overview of MacVector's alignment tools.

Related Topics.

Online Functional Domain Analysis (Interproscan)

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